Methods and compositions for producing labeled probe nucleic acids for use in array based comparative genomic hybridization applications

Abstract

Methods and compositions for producing labeled probe nucleic acids from genomic nucleic acid template are provided. In the subject methods, a conserved coding consensus region primer is employed to enzymatically generate a select set of labeled probe nucleic acids corresponding to coding regions of genes from a genomic template via a primer extension protocol. The subject methods find use in a variety of different applications, and are particularly suited for use in the preparation of labeled probe nucleic acids for use in array based comparative genomic hybridization applications. Also provided are kits for use in practicing the subject methods.

1. A method for comparing the relative copy number of nucleic acid sequences in two or more collections of nucleic acid molecules, the method comprising:
 (a) preparing at least a first collection of labeled nucleic acid probe molecules labeled with a first label and a second collection of labeled nucleic acid probe molecules labeled with a second label distinguishable from said first label, wherein each constituent member of said first and second collections of labeled nucleic acid probe molecules is prepared from a genomic nucleic acid template using a set of primers that includes at least one primer comprising a sequence of a conserved coding consensus region; 
 (b) contacting said first and second collections of labeled probe molecules with a plurality of target elements bound to a solid surface, each target element comprising a target nucleic acid; 
 (c) evaluating the relative binding of the first and second collections of labeled nucleic acid probe molecules to the same target nucleic acid to compare the relative copy number of nucleic acid sequences in said first and second collections of labeled nucleic acid probe molecules. 
 
     
     
       2. The method according to  claim 1 , wherein said sequence of a conserved coding consensus region comprises ATG. 
     
     
       3. The method according to  claim 2 , wherein said ATG comprising primer comprises a sequence of the formula:
   5′-(N)n-ATG-(N)n-3′, 
 wherein each N is independently any nucleotide residue and each n is independently 0 or an integer from 1 to 10. 
 
     
     
       4. The method according to  claim 1 , wherein said sequence of a conserved coding consensus region comprises a consensus splice site. 
     
     
       5. The method according to  claim 4 , wherein said consensus splice site is a 5′ consensus splice site or a 3′ consensus splice site. 
     
     
       6. The method of  claim 1 , wherein the first and second labels are fluorescent labels. 
     
     
       7. The method of  claim 1 , wherein the solid support is a plurality of beads. 
     
     
       8. The method of  claim 1 , wherein the solid support is glass. 
     
     
       9. The method of  claim 1 , wherein said plurality of target elements bound to a solid surface comprise an array. 
     
     
       10. The method of  claim 1 , wherein the first collection of labeled nucleic acids is from a test genome and the second collection of labeled nucleic acids is from a normal reference genome. 
     
     
       11. The method according to  claim 1 , wherein said sequence of a conserved coding consensus region is a human sequence. 
     
     
       12. The method according to  claim 1 , wherein said set of primers is not a random set of primers. 
     
     
       13. The method according to  claim 12 , wherein at least 5% of said set comprises primers that include a conserved coding consensus region. 
     
     
       14. The method according to  claim 1 , wherein said contacting step (b) occurs under low stringency conditions. 
     
     
       15. The method according to  claim 1 , wherein said method further comprises a data transmission step in which a result from said evaluating is transmitted from a first location to a second location. 
     
     
       16. A method comprising receiving data representing a result of said evaluation obtained by the method of  claim 1 .